eegdash 0.4.0.dev144__py3-none-any.whl → 0.4.0.dev153__py3-none-any.whl

eegdash/__init__.py

@@ -18,4 +18,4 @@ _init_mongo_client()
 
 __all__ = ["EEGDash", "EEGDashDataset", "EEGChallengeDataset", "preprocessing"]
 
-__version__ = "0.4.0.dev144"
+__version__ = "0.4.0.dev153"

eegdash/api.py

@@ -15,12 +15,9 @@ from pathlib import Path
 from typing import Any, Mapping
 
 import mne
-import numpy as np
-import xarray as xr
 from docstring_inheritance import NumpyDocstringInheritanceInitMeta
 from dotenv import load_dotenv
-from joblib import Parallel, delayed
-from mne_bids import find_matching_paths, get_bids_path_from_fname, read_raw_bids
+from mne_bids import find_matching_paths
 from pymongo import InsertOne, UpdateOne
 from rich.console import Console
 from rich.panel import Panel
@@ -328,38 +325,6 @@ class EEGDash:
                         f"Conflicting constraints for '{key}': disjoint sets {r_val!r} and {k_val!r}"
                     )
 
-    def load_eeg_data_from_bids_file(self, bids_file: str) -> xr.DataArray:
-        """Load EEG data from a local BIDS-formatted file.
-
-        Parameters
-        ----------
-        bids_file : str
-            Path to a BIDS-compliant EEG file (e.g., ``*_eeg.edf``, ``*_eeg.bdf``,
-            ``*_eeg.vhdr``, ``*_eeg.set``).
-
-        Returns
-        -------
-        xr.DataArray
-            EEG data with dimensions ``("channel", "time")``.
-
-        """
-        bids_path = get_bids_path_from_fname(bids_file, verbose=False)
-        raw_object = read_raw_bids(bids_path=bids_path, verbose=False)
-        eeg_data = raw_object.get_data()
-
-        fs = raw_object.info["sfreq"]
-        max_time = eeg_data.shape[1] / fs
-        time_steps = np.linspace(0, max_time, eeg_data.shape[1]).squeeze()  # in seconds
-
-        channel_names = raw_object.ch_names
-
-        eeg_xarray = xr.DataArray(
-            data=eeg_data,
-            dims=["channel", "time"],
-            coords={"time": time_steps, "channel": channel_names},
-        )
-        return eeg_xarray
-
     def add_bids_dataset(
         self, dataset: str, data_dir: str, overwrite: bool = True
     ) -> None:
@@ -423,39 +388,6 @@ class EEGDash:
             logger.info("Upserted: %s", result.upserted_count)
             logger.info("Errors: %s ", result.bulk_api_result.get("writeErrors", []))
 
-    def get(self, query: dict[str, Any]) -> list[xr.DataArray]:
-        """Download and return EEG data arrays for records matching a query.
-
-        Parameters
-        ----------
-        query : dict
-            MongoDB query used to select records.
-
-        Returns
-        -------
-        list of xr.DataArray
-            EEG data for each matching record, with dimensions ``("channel", "time")``.
-
-        Notes
-        -----
-        Retrieval runs in parallel. Downloaded files are read and discarded
-        (no on-disk caching here).
-
-        """
-        sessions = self.find(query)
-        results = []
-        if sessions:
-            logger.info("Found %s records", len(sessions))
-            results = Parallel(
-                n_jobs=-1 if len(sessions) > 1 else 1, prefer="threads", verbose=1
-            )(
-                delayed(downloader.load_eeg_from_s3)(
-                    downloader.get_s3path("s3://openneuro.org", session["bidspath"])
-                )
-                for session in sessions
-            )
-        return results
-
     def _add_request(self, record: dict):
         """Internal helper method to create a MongoDB insertion request for a record."""
         return InsertOne(record)
@@ -1016,3 +948,6 @@ class EEGDashDataset(BaseConcatDataset, metaclass=NumpyDocstringInheritanceInitM
                 )
             )
         return datasets
+
+
+__all__ = ["EEGDash", "EEGDashDataset"]

eegdash/bids_eeg_metadata.py

@@ -385,3 +385,11 @@ def enrich_from_participants(
     extras = participants_extras_from_tsv(bids_root, subject)
     attach_participants_extras(raw, description, extras)
     return extras
+
+
+__all__ = [
+    "participants_row_for_subject",
+    "participants_extras_from_tsv",
+    "attach_participants_extras",
+    "enrich_from_participants",
+]

eegdash/data_utils.py

@@ -672,3 +672,6 @@ class EEGBIDSDataset:
         for list_field in ["name", "type", "units"]:
             channel_tsv[list_field] = list(channel_tsv[list_field].values())
         return channel_tsv
+
+
+__all__ = ["EEGDashBaseDataset", "EEGBIDSDataset", "EEGDashBaseRaw"]

eegdash/downloader.py

@@ -10,15 +10,10 @@ between the EEGDash metadata database and the actual EEG data stored in the clou
 """
 
 import re
-import tempfile
 from pathlib import Path
 from typing import Any
-from urllib.parse import urlsplit
 
-import mne
-import numpy as np
 import s3fs
-import xarray as xr
 from fsspec.callbacks import TqdmCallback
 
 
@@ -108,80 +103,9 @@ def _filesystem_get(filesystem: s3fs.S3FileSystem, s3path: str, filepath: Path):
     return filepath
 
 
-def load_eeg_from_s3(s3path: str):
-    """Load EEG data from an S3 URI into an ``xarray.DataArray``.
-
-    Preserves the original filename, downloads sidecar files when applicable
-    (e.g., ``.fdt`` for EEGLAB, ``.vmrk``/``.eeg`` for BrainVision), and uses
-    MNE's direct readers.
-
-    Parameters
-    ----------
-    s3path : str
-        An S3 URI (should start with "s3://").
-
-    Returns
-    -------
-    xr.DataArray
-        EEG data with dimensions ``("channel", "time")``.
-
-    Raises
-    ------
-    ValueError
-        If the file extension is unsupported.
-
-    """
-    filesystem = get_s3_filesystem()
-    # choose a temp dir so sidecars can be colocated
-    with tempfile.TemporaryDirectory() as tmpdir:
-        # Derive local filenames from the S3 key to keep base name consistent
-        s3_key = urlsplit(s3path).path  # e.g., "/dsXXXX/sub-.../..._eeg.set"
-        basename = Path(s3_key).name
-        ext = Path(basename).suffix.lower()
-        local_main = Path(tmpdir) / basename
-
-        # Download main file
-        with (
-            filesystem.open(s3path, mode="rb") as fsrc,
-            open(local_main, "wb") as fdst,
-        ):
-            fdst.write(fsrc.read())
-
-        # Determine and fetch any required sidecars
-        sidecars: list[str] = []
-        if ext == ".set":  # EEGLAB
-            sidecars = [".fdt"]
-        elif ext == ".vhdr":  # BrainVision
-            sidecars = [".vmrk", ".eeg", ".dat", ".raw"]
-
-        for sc_ext in sidecars:
-            sc_key = s3_key[: -len(ext)] + sc_ext
-            sc_uri = f"s3://{urlsplit(s3path).netloc}{sc_key}"
-            try:
-                # If sidecar exists, download next to the main file
-                info = filesystem.info(sc_uri)
-                if info:
-                    sc_local = Path(tmpdir) / Path(sc_key).name
-                    with (
-                        filesystem.open(sc_uri, mode="rb") as fsrc,
-                        open(sc_local, "wb") as fdst,
-                    ):
-                        fdst.write(fsrc.read())
-            except Exception:
-                # Sidecar not present; skip silently
-                pass
-
-        # Read using appropriate MNE reader
-        raw = mne.io.read_raw(str(local_main), preload=True, verbose=False)
-
-        data = raw.get_data()
-        fs = raw.info["sfreq"]
-        max_time = data.shape[1] / fs
-        time_steps = np.linspace(0, max_time, data.shape[1]).squeeze()
-        channel_names = raw.ch_names
-
-        return xr.DataArray(
-            data=data,
-            dims=["channel", "time"],
-            coords={"time": time_steps, "channel": channel_names},
-        )
+__all__ = [
+    "download_s3_file",
+    "download_dependencies",
+    "get_s3path",
+    "get_s3_filesystem",
+]

eegdash/logging.py

@@ -31,3 +31,5 @@ root_logger.setLevel(logging.INFO)
 logger = logging.getLogger("eegdash")
 
 logger.setLevel(logging.INFO)
+
+__all__ = ["logger"]

eegdash/mongodb.py

@@ -75,3 +75,6 @@ class MongoConnectionManager:
                 except Exception:
                     pass
             cls._instances.clear()
+
+
+__all__ = ["MongoConnectionManager"]

eegdash/paths.py

@@ -37,3 +37,6 @@ def get_default_cache_dir() -> Path:
 
     # 3) Default to a project-local hidden folder
     return Path.cwd() / ".eegdash_cache"
+
+
+__all__ = ["get_default_cache_dir"]

eegdash/utils.py

@@ -19,3 +19,6 @@ def _init_mongo_client():
                 "mongodb+srv://eegdash-user:mdzoMjQcHWTVnKDq@cluster0.vz35p.mongodb.net/?retryWrites=true&w=majority&appName=Cluster0",
                 set_env=True,
             )
+
+
+__all__ = ["_init_mongo_client"]

{eegdash-0.4.0.dev144.dist-info → eegdash-0.4.0.dev153.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: eegdash
-Version: 0.4.0.dev144
+Version: 0.4.0.dev153
 Summary: EEG data for machine learning
 Author-email: Young Truong <dt.young112@gmail.com>, Arnaud Delorme <adelorme@gmail.com>, Aviv Dotan <avivd220@gmail.com>, Oren Shriki <oren70@gmail.com>, Bruno Aristimunha <b.aristimunha@gmail.com>
 License-Expression: GPL-3.0-only
@@ -35,7 +35,6 @@ Requires-Dist: python-dotenv
 Requires-Dist: s3fs
 Requires-Dist: scipy
 Requires-Dist: tqdm
-Requires-Dist: xarray
 Requires-Dist: h5io>=0.2.4
 Requires-Dist: pymatreader
 Requires-Dist: eeglabio
@@ -58,6 +57,7 @@ Requires-Dist: sphinx_gallery; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Requires-Dist: pydata-sphinx-theme; extra == "docs"
 Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
 Requires-Dist: sphinx-sitemap; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
 Requires-Dist: memory_profiler; extra == "docs"

{eegdash-0.4.0.dev144.dist-info → eegdash-0.4.0.dev153.dist-info}/RECORD

@@ -1,13 +1,13 @@
-eegdash/__init__.py,sha256=mb1qG2Bvohd8m8HMQlfoq8GO9ANnQZ3bnjL8QnJKlFU,704
-eegdash/api.py,sha256=OLQbpOoIZpZVJSss3imLFmN6d1Fpwk6tj-yRMQlr00Q,39429
-eegdash/bids_eeg_metadata.py,sha256=EFJ1grNcqS0eF0hg45F6St8gFc3Hlzsgccpr-9XTMZk,14153
+eegdash/__init__.py,sha256=kBtCi9ttHkz_WkW0JbaB8V8PAZJQ-nyEL6m8PhPHFYY,704
+eegdash/api.py,sha256=vcme_BXxc0KpyLwQfrzV7lojM0s16P7KPq-62Gu9ee4,37241
+eegdash/bids_eeg_metadata.py,sha256=0fA5FDM4OlSS83JziRI7-hPvh-KRvwKBpT1dMeB4znk,14307
 eegdash/const.py,sha256=-cwrtncqJHZ19lGf2MK-IgKy7hTMfb6H-CeL50Oonyg,7883
-eegdash/data_utils.py,sha256=s9FyPpsw32ndBsusL4TQX6rOsLEiN73RneEuXKffaYc,26477
-eegdash/downloader.py,sha256=TsoFDmzSBLiTwW_scfju4MXEIq088upHvdEfGw_c8WM,6256
-eegdash/logging.py,sha256=Tbz-zXaxvzZkYmrAQTEyFqevzWtM5QZPP6LL7XNy8d0,952
-eegdash/mongodb.py,sha256=0QpkAdwQOisbCr0-rd0wPFQiG0IT9h2Ae-CXYdrt65o,2430
-eegdash/paths.py,sha256=-bl81r7UyPr-Kq6V6j6h9Mq6dxg5T5EkBVJlOLmQecg,1217
-eegdash/utils.py,sha256=05MwB7Y447qkWfxCqgGy2DZUHPV1c1xvr3EUyhD0OHI,723
+eegdash/data_utils.py,sha256=5g88vIuU_KTixWF2BV6wtQTs8ba23OPIMkrsEklmiE8,26548
+eegdash/downloader.py,sha256=ukkol-2Y-8FGgociwJR-3TqBfvbUuCuMt2L6E_6baDY,3638
+eegdash/logging.py,sha256=Jux2A3YM9m2ksETErEfUG7wnB7jpJw6v1JH9tQuYVJc,974
+eegdash/mongodb.py,sha256=oXjiNLf0-46r_0RbxG8Y8wQZl8MIcfGQt4_qieU2MqU,2469
+eegdash/paths.py,sha256=4-ae23KeXMP5yaKAJCNW7pQGV19c00ll0EGElV2rZn8,1255
+eegdash/utils.py,sha256=e7LdirPY0dAfMZNWTbgAguqzu-dq0zo-mtXB9nIzf_c,758
 eegdash/dataset/__init__.py,sha256=HKDfV2DHBv63BqYLBWDMvU8jbFNRC7DqQbxL7RG1DKQ,863
 eegdash/dataset/dataset.py,sha256=e_rliu4E-uPtz_miUSzGukUahCHHhyXB2Gu3pm3cyHo,7062
 eegdash/dataset/dataset_summary.csv,sha256=a5Y21LmBPKLVRt5uKNXO7lSRDjsDmJLzv6-3HryF5JU,23614
@@ -30,8 +30,8 @@ eegdash/features/feature_bank/utils.py,sha256=DGh-Q7-XFIittP7iBBxvsJaZrlVvuY5mw-
 eegdash/hbn/__init__.py,sha256=hsI5pmIuYDzr--aE5UiToO-P9XL5fVRKahZzdsAodro,794
 eegdash/hbn/preprocessing.py,sha256=cfsLXnGuUaVJ3NhueDgmdc0w7jflmIi69occuB4bs7M,2609
 eegdash/hbn/windows.py,sha256=23KyVl0pQn4o40wM3Rsu8nl5tN-REAusU7wcv9L4a5U,10351
-eegdash-0.4.0.dev144.dist-info/licenses/LICENSE,sha256=asisR-xupy_NrQBFXnx6yqXeZcYWLvbAaiETl25iXT0,931
-eegdash-0.4.0.dev144.dist-info/METADATA,sha256=CgGdbNlkxb0Ako1Q1cwdwEotFGf-CBz2yEZm6WBMmlw,6776
-eegdash-0.4.0.dev144.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-eegdash-0.4.0.dev144.dist-info/top_level.txt,sha256=zavO69HQ6MyZM0aQMR2zUS6TAFc7bnN5GEpDpOpFZzU,8
-eegdash-0.4.0.dev144.dist-info/RECORD,,
+eegdash-0.4.0.dev153.dist-info/licenses/LICENSE,sha256=asisR-xupy_NrQBFXnx6yqXeZcYWLvbAaiETl25iXT0,931
+eegdash-0.4.0.dev153.dist-info/METADATA,sha256=zOk45lmQlvD-HY0SMqhzh-PFWnRoSuEFME-m95KCNcg,6804
+eegdash-0.4.0.dev153.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+eegdash-0.4.0.dev153.dist-info/top_level.txt,sha256=zavO69HQ6MyZM0aQMR2zUS6TAFc7bnN5GEpDpOpFZzU,8
+eegdash-0.4.0.dev153.dist-info/RECORD,,